diff --git a/Docker/Dockerfile b/Docker/Dockerfile new file mode 100644 index 0000000..94149b8 --- /dev/null +++ b/Docker/Dockerfile @@ -0,0 +1,17 @@ +FROM python:3.8.5 + +LABEL org.label-schema.vcs-url="https://github.com/tekpinar/correlationPlus" +LABEL org.label-schema.version="1.0.3" +LABEL org.label-schema.description="A Python API to plot and analyze dynamical correlations of proteins." +LABEL org.label-schema.docker.cmd="docker run -v ~:/home/correlationPlus correlation_plus " + +USER root + +RUN pip3 install numpy==1.19.1 matplotlib==3.3.0 scipy==1.5.2 networkx==2.4 biopython==1.77 prody==1.10.11 +RUN pip3 correlationPlus==0.1.3 +RUN useradd -m correlationPlus + +USER correlationPlus +WORKDIR /home/correlationPlus + +ENTRYPOINT ["/bin/sh", "-c" , "correlationPlus $0 $@"] \ No newline at end of file diff --git a/correlationPlus/__init__.py b/correlationPlus/__init__.py index 1f2ff28..b1ab941 100644 --- a/correlationPlus/__init__.py +++ b/correlationPlus/__init__.py @@ -34,5 +34,5 @@ __all__ = ['calculate', 'mapAnalysis', 'diffMap', 'centralityAnalysis'] -__version__ = '0.1.2' +__version__ = '0.1.3' diff --git a/correlationPlus/scripts/calculate.py b/correlationPlus/scripts/calculate.py index ee426b2..16bfa71 100644 --- a/correlationPlus/scripts/calculate.py +++ b/correlationPlus/scripts/calculate.py @@ -29,6 +29,7 @@ from correlationPlus.calculate import calcENMnDCC + def usage_calculateApp(): """ Show how to use this program! @@ -44,6 +45,7 @@ def usage_calculateApp(): -o: This will be your output data file. Default is correlationMap.dat. (Optional) """) + def handle_arguments_calculateApp(): method = None out_file = None @@ -92,6 +94,8 @@ def handle_arguments_calculateApp(): sel_type = "ndcc" return method, out_file, sel_type, pdb_file + + def calculateApp(): method, out_file, sel_type, pdb_file = handle_arguments_calculateApp() print(f""" @@ -106,7 +110,8 @@ def calculateApp(): #Read pdb file selectedAtoms = parsePDB(pdb_file, subset='ca') calcENMnDCC(selectedAtoms, saveMatrix=True, out_file=out_file, method=method, nmodes=100) - print("@> Correlation calculation finished succesfully!") + print("@> Correlation calculation finished successfully!") + if __name__ == "__main__": calculateApp() diff --git a/requirements.txt b/requirements.txt index 2691cba..bde6931 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,6 @@ -numpy -matplotlib -prody -scipy -networkx \ No newline at end of file +numpy==1.19.1 +matplotlib==3.3.0 +scipy==1.5.2 +networkx==2.4 +biopython==1.77 +prody==1.10.11 diff --git a/setup.py b/setup.py index 666f87f..b636184 100644 --- a/setup.py +++ b/setup.py @@ -30,6 +30,7 @@ version=cp_vers, description=" Python package to plot and analyze dynamical correlations maps of proteins.", long_description=open('README.md').read(), + long_description_content_type="text/markdown", author="Mustafa Tekpinar", author_email="tekpinar@buffalo.edu", url="https://github.com/tekpinar/correlationPlus", @@ -39,6 +40,7 @@ 'Development Status :: 4 - Beta', 'Environment :: Console', 'Operating System :: POSIX', + 'Operating System :: Microsoft :: Windows', 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.6', 'Programming Language :: Python :: 3.7',